Thats is a nice coop! A chicken garden.... what a novel idea. I'm stealing your idea and using it at some point. It'll probably have to be at our next house. Living in a neighborhood with covenants isnt as nice as we thought it would be. I miss my farm.
I would say probably rethinking the inside layout for better, more efficient use of the space. I would have put in 2 instead of 1 skylite. I'm not sure what else I would change, I think that's it.
I would be using hardware cloth to enclose the run instead of anything else, and the run would have been bigger. I would have run electricity out to the coop so that there was light out there (flashlights just don't cut it when I'm out in the coop at night). I would have created access to the nestboxes from the outside of the coop.
If only I had joined BYC sooner... Hee hee. All these great ideas!